[English] 日本語
Yorodumi
- PDB-6nvw: Crystal structure of penicillin G acylase from Bacillus megaterium -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6nvw
TitleCrystal structure of penicillin G acylase from Bacillus megaterium
Components(Penicillin G acylase) x 2
KeywordsHYDROLASE / penicillin / acylase
Function / homology
Function and homology information


penicillin amidase / penicillin amidase activity / antibiotic biosynthetic process / response to antibiotic / extracellular region / metal ion binding
Similarity search - Function
Penicillin G acylase, C-terminal / Penicillin G acylase, beta-roll domain / Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region / Penicillin/GL-7-ACA/AHL acylase / Penicillin/GL-7-ACA/AHL/aculeacin-A acylase / Penicillin amidase type, domain 1 / Penicillin amidase type, N-terminal domain, B-knob / Penicillin amidase type, A-knob / Penicillin amidase / Aminohydrolase, N-terminal nucleophile (Ntn) domain ...Penicillin G acylase, C-terminal / Penicillin G acylase, beta-roll domain / Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region / Penicillin/GL-7-ACA/AHL acylase / Penicillin/GL-7-ACA/AHL/aculeacin-A acylase / Penicillin amidase type, domain 1 / Penicillin amidase type, N-terminal domain, B-knob / Penicillin amidase type, A-knob / Penicillin amidase / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Penicillin G acylase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.203 Å
AuthorsBlankenfeldt, W.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSPP1934 Germany
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2019
Title: Crystal structures and protein engineering of three different penicillin G acylases from Gram-positive bacteria with different thermostability.
Authors: Mayer, J. / Pippel, J. / Gunther, G. / Muller, C. / Lauermann, A. / Knuuti, T. / Blankenfeldt, W. / Jahn, D. / Biedendieck, R.
History
DepositionFeb 5, 2019Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 20, 2019Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.process_site
Revision 1.3May 15, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Penicillin G acylase
B: Penicillin G acylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,0094
Polymers85,9282
Non-polymers802
Water4,612256
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11800 Å2
ΔGint-100 kcal/mol
Surface area27970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.238, 77.961, 84.086
Angle α, β, γ (deg.)90.000, 101.670, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Penicillin G acylase / Penicillin G amidase / Penicillin G amidohydrolase


Mass: 24452.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Gene: pac, pga / Production host: Bacillus megaterium (bacteria) / References: UniProt: Q60136, penicillin amidase
#2: Protein Penicillin G acylase / Penicillin G amidase / Penicillin G amidohydrolase


Mass: 61475.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Gene: pac, pga / Production host: Bacillus megaterium (bacteria) / References: UniProt: Q60136, penicillin amidase
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.46 %
Crystal growTemperature: 309 K / Method: vapor diffusion, sitting drop / Details: 200 mM MgCl2, 20% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.0003 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0003 Å / Relative weight: 1
ReflectionResolution: 2.2→46.032 Å / Num. obs: 25584 / % possible obs: 68.4 % / Redundancy: 6.6 % / Net I/σ(I): 9
Reflection shellResolution: 2.2→2.38 Å

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XDSdata reduction
PHASERphasing
PHENIXdev_3386refinement
PDB_EXTRACT3.24data extraction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.203→46.032 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 31.55
RfactorNum. reflection% reflection
Rfree0.2747 1210 4.79 %
Rwork0.2146 --
obs0.2175 25271 67.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 137.03 Å2 / Biso mean: 42.0979 Å2 / Biso min: 4.06 Å2
Refinement stepCycle: final / Resolution: 2.203→46.032 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5791 0 2 256 6049
Biso mean--40.08 23.63 -
Num. residues----719
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2034-2.29160.854590.40021531624
2.2916-2.39590.312640.28681218128231
2.3959-2.52220.37291060.29211928203449
2.5222-2.68020.29141350.28162526266164
2.6802-2.88710.34931680.27023037320577
2.8871-3.17760.32351780.25333510368889
3.1776-3.63720.26191690.22313775394495
3.6372-4.58190.26891800.18373869404997
4.5819-46.04170.20332010.161640454246100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.38472.27640.76963.71221.49373.4562-0.2773-0.22090.4076-0.2272-0.2389-0.193-0.58580.46360.30080.2934-0.0126-0.10340.26890.03710.42229.880324.4189-34.8126
21.0871-0.319-0.75770.946-0.36051.4487-0.26710.02640.1681-0.0847-0.03440.02520.0603-0.09050.0327-0.0438-0.0393-0.25590.1072-0.05640.2802-10.026223.1509-22.4397
33.74340.8359-0.4860.97070.6631.6770.0631-0.3716-0.01420.0396-0.05580.0045-0.120.629-0.00590.4257-0.0121-0.16820.2866-0.00970.2775-2.922826.9541-7.4878
42.70580.3750.24682.8680.01462.3076-0.2733-0.15780.77090.1261-0.1462-0.1599-0.48320.34970.29790.1812-0.1155-0.20930.17930.00130.40031.730531.4719-24.3822
57.291-3.84172.50834.4086-0.3354.95340.23570.70430.1947-0.1571-0.1457-0.03610.07960.30270.1480.3130.0408-0.19870.1111-0.00510.3962-14.021629.0335-37.0525
61.2101-1.60170.36143.3603-1.01060.8953-0.1075-0.11290.24560.24-0.02890.3431-0.1192-0.1770.02670.23910.0491-0.09050.14420.0360.531-13.164230.4368-26.1474
71.05251.3017-0.89252.7559-1.46070.95330.0422-0.0496-0.1263-0.19390.03770.34810.03130.01770.02070.1610.0061-0.09840.1268-0.12940.2236-6.815716.3816-14.1001
81.55070.18690.13161.44370.32240.259-0.1162-0.30360.03030.52160.01130.3888-0.1315-0.3437-0.04270.26050.0032-0.02730.23730.02670.2458-20.0505-8.1180.524
92.0279-1.1332-1.67086.00670.2046.2549-0.4905-0.3893-0.3663-0.3875-0.33970.15390.35710.34170.37370.10610.0523-0.05150.19020.03210.20530.6153-10.3104-7.3094
100.5116-0.1333-0.3020.67330.1550.9727-0.0705-0.10110.08920.1068-0.0391-0.1543-0.14950.03360.08720.1501-0.0193-0.14470.1632-0.0190.2835-3.514213.3096-11.6238
110.33730.036-0.15890.84760.08330.4239-0.0217-0.01-0.02150.0376-0.0593-0.12050.11710.11470.06920.1870.0464-0.10960.16680.05150.2973-1.4977-9.439-17.289
121.5793-1.2283-0.50511.57461.35251.7206-0.0708-0.1477-0.34060.096-0.08090.22620.1156-0.28150.13320.3108-0.0523-0.10590.11270.01760.2918-17.0646-17.1919-13.3434
130.9830.4885-0.06991.55190.09760.34680.2335-0.0958-0.00320.0332-0.20760.11150.11890.06790.02380.2005-0.0193-0.06210.05650.01520.2265-13.4687-7.993-30.2365
140.9192-0.19820.15771.46330.37581.0143-0.03180.24230.2418-0.5845-0.0091-0.2827-0.11220.16760.03420.2359-0.0385-0.02050.11620.06520.2641.768111.4008-38.7143
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 24 )A3 - 24
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 72 )A25 - 72
3X-RAY DIFFRACTION3chain 'A' and (resid 73 through 88 )A73 - 88
4X-RAY DIFFRACTION4chain 'A' and (resid 89 through 111 )A89 - 111
5X-RAY DIFFRACTION5chain 'A' and (resid 112 through 123 )A112 - 123
6X-RAY DIFFRACTION6chain 'A' and (resid 124 through 132 )A124 - 132
7X-RAY DIFFRACTION7chain 'A' and (resid 133 through 151 )A133 - 151
8X-RAY DIFFRACTION8chain 'A' and (resid 152 through 179 )A152 - 179
9X-RAY DIFFRACTION9chain 'A' and (resid 180 through 194 )A180 - 194
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 187 )B1 - 187
11X-RAY DIFFRACTION11chain 'B' and (resid 188 through 345 )B188 - 345
12X-RAY DIFFRACTION12chain 'B' and (resid 346 through 404 )B346 - 404
13X-RAY DIFFRACTION13chain 'B' and (resid 405 through 473 )B405 - 473
14X-RAY DIFFRACTION14chain 'B' and (resid 474 through 527 )B474 - 527

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more